PDB-4g9h: Crystal structure of glutahtione s-transferase homolog from yersi...

ID or keywords:

Entry

Database: PDB / ID: 4g9h

Title

Crystal structure of glutahtione s-transferase homolog from yersinia pestis, target EFI-501894, with bound glutathione

Components

Glutathione S-transferase

Keywords

TRANSFERASE / GST / glutathione S-transferase / enzyme function initiative / EFI / Structural Genomics

Function / homology

Function and homology information

Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...
Similarity search - Domain/homology

Biological species

Yersinia pestis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...

Citation

Journal: To be Published
Title: Crystal structure of glutahtione s-transferase homolog from yersinia pestis, target efi-501894, with bound glutathione
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / ...

History

Deposition	Jul 23, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 15, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4g9h.cif.gz	180.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4g9h.ent.gz	145.4 KB	Display	PDB format
PDBx/mmJSON format	4g9h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4g9h_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	4g9h_full_validation.pdf.gz	1 MB	Display
Data in XML	4g9h_validation.xml.gz	19.4 KB	Display
Data in CIF	4g9h_validation.cif.gz	27.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g9/4g9h ftp://data.pdbj.org/pub/pdb/validation_reports/g9/4g9h	HTTPS FTP

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Related structure data

Related structure data	2pmtS S: Starting model for refinement
Similar structure data	4gci-d 2vcq-2 5uas-2 2imk-d 3ee2-d 5ywx-2 6w8h-d 3f6d-d 1pd2-d 1f2e-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: EFI-501894

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (10) #255 - Mar 2021 Cisplatin and DNA similarity (9)

Deposited unit

A: Glutathione S-transferase

B: Glutathione S-transferase

hetero molecules

48.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	87.945, 87.945, 148.786
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Details

biological unit is dimer

#1: Protein	Glutathione S-transferase / Glutathionine S-transferase Mass: 23791.279 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: gst, gst2, y1968, YP_2153 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8D0L3
#2: Chemical	ChemComp-GSH / GLUTATHIONE Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.02 Å³/Da / Density % sol: 59.31 %
Crystal grow	Temperature: 298 K / Method: sitting drop vapor diffuction / pH: 7.5 Details: Protein (10 mM Hepes pH 7.5, 100 mM NaCl); Reservoir (0.6 M NaCl, 0.1 M MES pH 6.5, 20% Peg4000); Cryoprotection (Reservoir, + 20% glycerol), sitting drop vapor diffuction, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
Detector	Type: RAYONIX 225 HE / Detector: CCD / Date: Jul 9, 2012 / Details: MIRRORS
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.1→75.709 Å / Num. all: 34816 / Num. obs: 34816 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / R_merge(I) obs: 0.107 / R_sym value: 0.107 / Net I/σ(I): 14.8
Reflection shell	Resolution: 2.1→2.13 Å / Redundancy: 9.7 % / R_merge(I) obs: 0.791 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2806 / R_sym value: 0.791 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
SCALA		data scaling
PHENIX	1.8_1069	refinement
PDB_EXTRACT	3.11	data extraction
MOSFLM		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2PMT

2pmt

Resolution: 2.1→34.77 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8536 / SU ML: 0.19 / σ(F): 0 / σ(I): 0 / Phase error: 20.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2164	1751	5.04 %	RANDOM
R_work	0.1759	-	-	-
all	0.1779	34755	-	-
obs	0.1779	34755	99.8 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 107.26 Å² / B_iso mean: 36.4998 Å² / B_iso min: 11.23 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→34.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3196	0	46	248	3490

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3383
X-RAY DIFFRACTION	f_angle_d	1.019	4599
X-RAY DIFFRACTION	f_chiral_restr	0.064	515
X-RAY DIFFRACTION	f_plane_restr	0.004	593
X-RAY DIFFRACTION	f_dihedral_angle_d	14.756	1280

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1-2.1568	0.2648	136	0.2224	2487	2623	100
2.1568-2.2202	0.2839	129	0.2093	2491	2620	100
2.2202-2.2919	0.2691	120	0.217	2476	2596	100
2.2919-2.3738	0.2707	116	0.1892	2539	2655	100
2.3738-2.4688	0.2286	127	0.1966	2499	2626	100
2.4688-2.5811	0.236	163	0.1783	2476	2639	100
2.5811-2.7172	0.249	133	0.181	2498	2631	100
2.7172-2.8873	0.2364	151	0.1783	2520	2671	100
2.8873-3.1101	0.2465	139	0.187	2533	2672	100
3.1101-3.4229	0.1891	142	0.1782	2537	2679	100
3.4229-3.9176	0.1917	147	0.1678	2564	2711	100
3.9176-4.9335	0.1848	128	0.1453	2625	2753	100
4.9335-34.7749	0.1967	120	0.1727	2759	2879	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.703	0.3747	0.0681	0.6832	-0.1211	0.394	-0.0296	-0.1633	0.2635	0.2639	-0.0463	-0.3942	-0.3982	0.4961	-0.1216	0.2792	-0.3046	-0.3705	0.2397	0.011	0.4297	47.7014	97.713	30.2589
2	0.5482	0.0328	0.3862	0.0023	0.0217	0.2713	-0.0429	-0.2602	0.2787	0.2121	0.0676	-0.2661	-0.2934	0.228	-0.0152	1.1616	-0.2038	-0.2077	0.5357	-0.1641	0.4603	43.2643	106.3733	42.1844
3	2.4975	1.8416	0.3295	3.7943	-0.1035	0.093	-0.1359	0.0492	0.1329	0.0293	-0.0119	-0.1284	-0.032	0.0406	-0.1022	0.501	-0.3149	-0.0382	0.2689	-0.109	0.4631	44.0772	108.5088	27.7338
4	1.4732	0.5717	-0.0112	1.3752	-0.4064	1.7728	-0.0333	0.2821	-0.0379	0.0498	0.0467	-0.1394	-0.1489	0.1455	0.0115	0.1921	-0.0425	0.0157	0.173	-0.0008	0.1772	34.7896	95.9255	19.1485
5	0.6165	0.0745	-0.7541	0.0402	-0.3683	3.3115	-0.2635	-0.1778	0.2334	0.3141	0.0153	-0.0818	-0.3365	0.0288	0.0622	0.5479	0.0724	0.0238	0.212	0.0369	0.2647	28.9206	92.7569	43.4382
6	1.0207	-0.4219	-1.4094	1.4075	2.211	5.9007	-0.117	-0.1079	0.0572	0.3912	0.1684	0.3154	-0.1101	-0.4938	-0.0031	0.4014	0.0671	0.0739	0.2312	0.0648	0.2486	23.0622	84.3797	37.4709
7	2.1158	0.5449	-0.171	2.1474	-0.1181	1.3625	-0.191	0.1085	-0.222	0.0415	-0.011	-0.292	0.2178	0.2175	0.1378	0.2117	0.0142	-0.0018	0.1278	0.0088	0.2231	35.9847	85.2646	25.5516
8	1.8816	0.8876	1.1577	1.7857	0.1711	2.3706	-0.0763	0.0262	-0.2774	0.2388	0.1811	-0.1525	0.3089	-0.1884	-0.0459	0.3522	0.0443	-0.0597	0.1416	0.011	0.2242	33.2002	77.5939	32.5871
9	2.2218	-0.4267	0.2888	0.723	0.154	0.3592	-0.0145	-0.2372	0.0138	0.1974	0.0181	-0.3001	0.0659	0.2647	-0.0726	0.1811	0.0329	-0.1808	0.5223	0.1764	0.6657	49.4606	87.2075	31.5449
10	0.7406	0.2697	0.0788	1.8174	0.1514	1.065	-0.0145	0.0333	-0.3589	-0.0157	-0.0961	0.7735	0.2597	-0.4418	0.0561	0.2409	-0.0535	0.045	0.2323	0.0056	0.433	10.3756	96.4208	20.8364
11	2.3128	0.2053	0.582	1.9946	1.659	1.4539	0.1914	0.3836	-0.2117	-0.0593	-0.1354	0.1602	0.0817	-0.0494	-0.0408	0.3096	-0.079	-0.016	0.2735	-0.0449	0.2043	17.6521	93.3969	13.8731
12	1.7289	0.341	-0.2296	1.2952	0.0554	1.3677	-0.0213	0.1947	0.136	-0.079	0.0045	-0.2622	-0.4487	0.1611	0.0409	0.28	-0.0148	0.0236	0.1296	0.0271	0.1976	27.597	107.0017	19.2282
13	1.5334	-0.0815	0.1167	0.0814	0.2945	1.1667	-0.0165	-0.3621	-0.4965	0.1743	0.1099	0.3683	0.2452	-0.2574	0.0249	0.4363	0.0271	0.1765	0.3036	0.1269	0.3399	16.5301	97.9498	40.4006
14	2.0178	0.3285	0.177	2.8713	-1.4426	1.3083	-0.3272	-0.7923	-0.2135	0.5568	0.1946	0.149	-0.1097	0.1882	0.117	0.606	0.1836	0.0529	0.3847	0.0128	0.2289	22.8126	107.4726	43.9222
15	3.0001	1.1076	-0.1765	4.8322	1.6806	1.8515	-0.1018	0.0198	0.4302	-0.0057	0.0341	-0.2146	-0.3843	0.2633	0.0373	0.4942	-0.0691	-0.0367	0.1496	-0.016	0.2915	25.9707	119.0988	25.3801
16	1.1396	0.4101	-0.278	1.1069	-0.7672	2.1245	-0.1114	-0.2822	-0.0684	0.3342	0.1022	0.0962	-0.222	-0.2653	-0.0412	0.3061	0.0389	0.0546	0.1785	0.0357	0.1665	16.8085	108.8116	30.7046
17	1.7482	0.1815	0.7758	1.8076	0.0522	3.088	-0.1739	-0.3328	0.1477	0.583	0.0827	-0.0771	-0.3419	0.0906	0.0233	0.5421	0.1556	0.0239	0.287	-0.0197	0.2123	17.6163	117.0835	36.801
18	1.8752	1.0453	0.5001	4.0996	-0.2794	2.1678	-0.0107	-0.2148	-0.2274	0.0597	0.0585	0.571	-0.0069	-0.2743	-0.0628	0.1767	0.0259	0.0483	0.2002	0.0787	0.2964	7.3722	111.1759	22.0555

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 30 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 31 through 54 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 55 through 66 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 105 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 106 through 119 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 120 through 141 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 142 through 168 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 169 through 188 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 189 through 201 )	A
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 0 through 54 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 55 through 66 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 67 through 105 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 106 through 119 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 120 through 141 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 142 through 153 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 154 through 168 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 169 through 188 )	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 189 through 201 )	B

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